St. Louis, Missouri, USA
November 10, 2011
The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has selected two projects from a highly competitive pool of applications, submitted by Danforth Plant Science Center Principal Investigators, Dr. Thomas Brutnell and Dr. Todd Mockler as part of its 2012 Community Sequencing Program (CSP).
The 2012 CSP call invited researchers to submit proposals for projects that advance capabilities in fields such as plant-microbe interactions, microbes involved in carbon capture and greenhouse gas emission, and metagenomics—the characterization of complex collections of microbes from particular environmental niches. This data will enhance research projects that aim to improve biofuel feedstock production, focusing on the potential of microorganisms to improve feedstock growth and prevent devastating diseases that hinder yields.
The project proposed by Drs. Brutnell and Mockler will develop sequence-based community tools for Setaria viridis-a model genetic system for bioenergy grasses. Brutnell and Mockler and colleagues Jeff Bennetzen (University of GA), Katrien Devos (University of GA), Elizabeth Kellogg (University of Missouri-St. Louis) and Andrew Doust (Oklahoma State University) will use high- throughput sequencing technology to rapidly advance genetic resources in Setaria viridis (also known as green bristlegrass). Setaria is rapidly emerging as a model system for bioenergy grasses as it is closely related to the primary bioenergy feedstock crops such as switchgrass, Miscanthus and sugarcane, but is a much more manageable genetic system. This project will include providing sequence blueprints for more than 50 diverse varieties of Setaria as well as providing the data to facilitate the development of mutagenized populations and lines that can be used to map genetic variation. The development of these genetic resources will enable scientists to identify genes that contribute to a number of traits that are essential to develop efficient biomass production including increased stress tolerance, water and nitrogen use efficiency and biomass production.
The second project of which Dr. Mockler is a co-PI with Dr. Samuel Hazen at the University of Massachusetts; will create a library of grass transcription factors for the energy crop model system Brachypodium distachyon. Brachypodium serves as a model for potential energy crops such as switchgrass, sorghum, and Miscanthus, as well as for the cereal crops that constitute a large part of the world’s diet. Transcription factors are proteins that regulate gene expression, and the Brachypodium transcription factors targeted in this project are implicated in grass cell wall biosynthesis and the regulation of growth and biomass accumulation by light. Hazen, Mockler, and collaborator Dr. Steve Kay at the University of California San Diego will use this project as the cornerstone of a new high-throughout platform for analyzing protein-DNA interactions for the purpose of understanding important traits in grass species.
These grants will provide a huge boost to the development of these two model grasses and will greatly accelerate the ability of scientists to translate basic scientific discoveries into application.
“The Enterprise Rent-A-Car Institute for Renewable Fuels has a strong foundation in developing algal and seed oil biofuels. These new grants will expand the Institute’s portfolio to include development of model systems for lignocellulosic feedstocks,” said Brutnell. “I am particularly excited about the prospects of the Danforth Center becoming a leader in molecular tool development for these model grasses.”
A total of 41 proposals were approved from the 152 submitted, culled from the 188 letters of intent originally received. The projects were then reviewed and approved by an outside panel before being vetted by the DOE.
The total allocation for the coming year’s CSP portfolio will exceed 30 trillion bases (terabases or Tb), a 100-fold increase compared with just two years ago, when just a third of a terabase was allocated to more than 70 projects. This amounts to the equivalent of at least 10,000 human genomes in data.
“These selections truly take advantage of the DOE JGI’s massive-scale sequencing and data analysis capabilities,” said Eddy Rubin, DOE JGI Director. “The projects span the globe and the unexplored branches of the tree of life, and promise to yield a better understanding of the interplay between climate, ecosystem and organism.”
For the complete list of CSP 2012 sequencing projects please visit, http://www.jgi.doe.gov/sequencing/cspseqplans2012.html.
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